Swivel Motion Research Articles

Negative charge in the RACK1 loop broadens the translational capacity of the human ribosome.

SUMMARYAlthough the roles of initiation factors, RNA binding proteins, and RNA elements in regulating translation are well defined, how the ribosome functionally diversifies remains poorly understood. In their human hosts, poxviruses phosphorylate serine 278 (S278) at the tip of a loop domain in the small subunit ribosomal protein RACK1, thereby mimicking negatively charged residues in the RACK1 loops of dicot plants and protists to stimulate translation of transcripts with 5′ poly(A) leaders. However, how a negatively charged RACK1 loop affects ribosome structure and its broader translational output is not known. Here, we show that although ribotoxin-induced stress signaling and stalling on poly(A) sequences are unaffected, negative charge in the RACK1 loop alters the swivel motion of the 40S head domain in a manner similar to several internal ribosome entry sites (IRESs), confers resistance to various protein synthesis inhibitors, and broadly supports noncanonical modes of translation.

An Incremental Learning Framework for Human-Like Redundancy Optimization of Anthropomorphic Manipulators

Recently, the human-like behavior on the anthropomorphic robot manipulator is increasingly accomplished by the kinematic model establishing the relationship of an anthropomorphic manipulator and human arm motions. Notably, the growth and broad availability of advanced data science techniques facilitate the imitation learning process in anthropomorphic robotics. However, the enormous dataset causes the labeling and prediction burden. In this article, the swivel motion reconstruction approach was applied to imitate human-like behavior using the kinematic mapping in robot redundancy. For the sake of efficient computing, a novel incremental learning framework that combines an incremental learning approach with a deep convolutional neural network is proposed for fast and efficient learning. The algorithm exploits a novel approach to detect changes from human motion data streaming and then evolve its hierarchical representation of features. The incremental learning process can fine-tune the deep network only when model drifts detection mechanisms are triggered. Finally, we experimentally demonstrated this neural network's learning procedure and translated the trained human-like model to manage the redundancy optimization control of an anthropomorphic robot manipulator (LWR4+, KUKA, Germany). This approach can hold the anthropomorphic kinematic structure-based redundant robots. The experimental results showed that our architecture could not only enhance the regression accuracy but also significantly reduce the processing time of learning human motion data.

Acidic pH-Induced Conformational Changes in Chikungunya Virus Fusion Protein E1: a Spring-Twisted Region in the Domain I-III Linker Acts as a Hinge Point for Swiveling Motion of Domains.

Chikungunya virus (CHIKV), a mosquito-transmitted alphavirus, enters a cell through endocytosis, followed by viral and cell membrane fusion. The fusion protein, E1, undergoes an acid pH-induced pre- to postfusion conformation change during membrane fusion. As part of the conformation change, E1 dissociates from the receptor-binding protein, E2, and swivels its domains I and II over domain III to form an extended intermediate and then eventually to form a postfusion hairpin homotrimer. In this study, we tested if the domain I-III linker acts as a "hinge" for the swiveling motion of E1 domains. We found a conserved spring-twisted structure in the linker, stabilized by a salt bridge between a conserved arginine-aspartic acid pair, as a "hinge point" for domain swiveling. Molecular dynamics (MD) simulation of the CHIKV E1 or E2-E1 structure predicted that the spring-twisted region untwists at pH 5.5. Corroborating the prediction, introduction of a "cystine staple" at the hinge point, replacing the conserved arginine-aspartic acid pair with cysteine residues, resulted in loss of fusion activity of E1. MD simulation also predicted domain I-III swiveling at acidic pH. We tested if breaking the His 331-Lys 16 H bond between domains I and III, seen only in the prefusion conformation, is important for domain swiveling. When domains I and III are "stapled" by introducing a disulfide bond in between, E1 showed loss of fusion activity, implying that domain I and III dissociation is a critical acid pH-induced step in membrane fusion. However, replacement of His 331 with an acidic residue did not affect the pH threshold for fusion, suggesting His 331 is not an acid-sensing residue.IMPORTANCEAedes mosquito-transmitted viruses such as the Zika, dengue, and chikungunya viruses have spread globally. CHIKV, similar to many other enveloped viruses, enters cells in sequential steps: step 1 involves receptor binding followed by endocytosis, and step 2 involves viral-cell membrane fusion in the endocytic vesicle. The viral envelope surface protein, E1, performs membrane fusion. E1 is triggered to undergo conformational changes by acidic pH of the maturing endosome. Different domains of E1 rearrange during the pre- to postfusion conformation change. Using in silico analysis of the E1 structure and different biochemical experiments, we explained a structural mechanism of key conformational changes in E1 triggered by acidic pH. We noted two important structural changes in E1 at acidic pH. In the first, a spring-twisted region in a loop connecting two domains (I and III) untwists, bringing a swiveling motion of domains on each other. In the second, breaking of interactions between domains I and III and domain separation are required for membrane fusion. This knowledge will help devise new therapeutic strategies to block conformation changes in E1 and thus viral entry.

The Oligomerization Landscape of Histones

In eukaryotes, DNA is packaged within nucleosomes. The DNA of each nucleosome is typically centered around an octameric histone protein core: one central tetramer plus two separate dimers. Studying the assembly mechanisms of histones is essential for understanding the dynamics of entire nucleosomes and higher-order DNA packaging. Here, we investigate canonical histone assembly and that of the centromere-specific histone variant, centromere protein A (CENP-A), using molecular dynamics simulations. We quantitatively characterize their thermodynamical and dynamical features, showing that two H3/H4 dimers form a structurally floppy, weakly bound complex, the latter exhibiting large instability around the central interface manifested via a swiveling motion of two halves. This finding is consistent with the recently observed DNA handedness flipping of the tetrasome. In contrast, the variant CENP-A encodes distinctive stability to its tetramer with a rigid but twisted interface compared to the crystal structure, implying diverse structural possibilities of the histone variant. Interestingly, the observed tetramer dynamics alter significantly and appear to reach a new balance when H2A/H2B dimers are present. Furthermore, we found that the preferred structure for the (CENP-A/H4)2 tetramer is incongruent with the octameric structure, explaining many of the unusual dynamical behaviors of the CENP-A nucleosome. In all, these data reveal key mechanistic insights and structural details for the assembly of canonical and variant histone tetramers and octamers, providing theoretical quantifications and physical interpretations for longstanding and recent experimental observations. Based on these findings, we propose different chaperone-assisted binding and nucleosome assembly mechanisms for the canonical and CENP-A histone oligomers.

Improved Human–Robot Collaborative Control of Redundant Robot for Teleoperated Minimally Invasive Surgery

An improved human–robot collaborative control scheme is proposed in a teleoperated minimally invasive surgery scenario, based on a hierarchical operational space formulation of a seven-degree-of-freedom redundant robot. Redundancy is exploited to guarantee a remote center of motion (RCM) constraint and to provide a compliant behavior for the medical staff. Based on the implemented hierarchical control framework, an RCM constraint and a safe constraint are applied to the null-space motion to achieve the surgical tasks with human–robot interaction. Due to the physical interactions, safety and accuracy of the surgery may be affected. The control framework integrates an adaptive compensator to enhance the accuracy of the surgical tip and to maintain the RCM constraint in a decoupled way avoiding any physical interactions. The system performance is verified on a patient phantom. Compared with the methods proposed in the literature, results show that the accuracy of both the RCM constraint and the surgical tip is improved. The compliant swivel motion of the robot arm is also constrained in a defined area, and the interaction force on the abdominal wall becomes smaller.

Deep Neural Network Approach in Human-Like Redundancy Optimization for Anthropomorphic Manipulators

Human-like behavior has emerged in the robotics area for improving the quality of Human-Robot Interaction (HRI). For the human-like behavior imitation, the kinematic mapping between a human arm and robot manipulator is one of the popular solutions. To fulfill this requirement, a reconstruction method called swivel motion was adopted to achieve human-like imitation. This approach aims at modeling the regression relationship between robot pose and swivel motion angle. Then it reaches the human-like swivel motion using its redundant degrees of the manipulator. This characteristic holds for most of the redundant anthropomorphic robots. Although artificial neural network (ANN) based approaches show moderate robustness, the predictive performance is limited. In this paper, we propose a novel deep convolutional neural network (DCNN) structure for reconstruction enhancement and reducing online prediction time. Finally, we utilized the trained DCNN model for managing redundancy control a 7 DoFs anthropomorphic robot arm (LWR4+, KUKA, Germany) for validation. A demonstration is presented to show the human-like behavior on the anthropomorphic manipulator. The proposed approach can also be applied to control other anthropomorphic robot manipulators in industry area or biomedical engineering.

Ribosome Structure, Function, and Early Evolution.

Ribosomes are among the largest and most dynamic molecular motors. The structure and dynamics of translation initiation and elongation are reviewed. Three ribosome motions have been identified for initiation and translocation. A swivel motion between the head/beak and the body of the 30S subunit was observed. A tilting dynamic of the head/beak versus the body of the 30S subunit was detected using simulations. A reversible ratcheting motion was seen between the 30S and the 50S subunits that slide relative to one another. The 30S–50S intersubunit contacts regulate translocation. IF2, EF-Tu, and EF-G are homologous G-protein GTPases that cycle on and off the same site on the ribosome. The ribosome, aminoacyl-tRNA synthetase (aaRS) enzymes, transfer ribonucleic acid (tRNA), and messenger ribonucleic acid (mRNA) form the core of information processing in cells and are coevolved. Surprisingly, class I and class II aaRS enzymes, with distinct and incompatible folds, are homologs. Divergence of class I and class II aaRS enzymes and coevolution of the genetic code are described by analysis of ancient archaeal species.

Safety-enhanced Collaborative Framework for Tele-operated Minimally Invasive Surgery Using a 7-DoF Torque-controlled Robot

In this paper, a safety-enhanced collaborative control framework is proposed for tele-operated minimally invasive surgery (MIS) using a redundant 7-DoF serial robot. The redundant manipulators offer a safe physical collaborative flexible workspace for nurse or surgeon (assisting physicians, patient support) undergoing surgery. The novel framework integrates a Cartesian compliance control strategy to guarantee that the tele-operated surgical tool always goes through the trocar position, and a safety-enhanced null-space collaborative strategy to constrain the swivel motion in an assumed safe range. Two event-based operative procedures (hands-on motion and teleoperation) are performed in torque level to achieve the whole surgical task. Finally, experimental studies with virtual surgical tasks were conducted to validate the effectiveness of the proposed framework, using the KUKA LWR 4+ robot and Sigma 7 master device. It provided an online flexible and safe collaborative way without degradation of the quality of the surgical task.

Exaggerated Swivel Motions of the Small Subunit Head Domain are Required for tRNA Translocation through the Bacterial Ribosome

Translocation of tRNA through the ribosome is essential for protein synthesis and for maintaining the open reading frame of mRNA translation. Translocation is associated with two large-scale rearrangements within the ribosome: an intersubunit rotation of the small subunit relative to the large subunit (rotation); and an intrasubunit rotation of small subunit head relative to its body (head swivel). Recent single-molecule FRET studies (smFRET) suggested that exaggerated head swivel motions accompany the translocation reaction coordinate. Here, we integrate molecular dynamics simulations of the 70S ribosome translocation complex with single molecule FRET studies to more fully characterize the conformational changes in the ribosome accompanying translocation, and the transit of key intermediates that have recently been identified by structural and smFRET investigations. By explicitly incorporating FRET labels into the simulations, we obtain configurations of the ribosome highly consistent with measured FRET efficiencies for each translocation intermediate. We find that a larger amplitude head swivel configuration (‘super swivel’) satisfies the constraints of FRET efficiency and conformational changes predicted to accompany translocation. In so doing, our study supports a simplified translocation pathway consistent with extant structural data and the order of events during and the geometric constraints predicted by recent smFRET initiatives. Our simulations also characterize the influence of dye flexibility on the smFRET distance estimates.

On the potential alternate binding change mechanism in a dimeric structure of Pyruvate Phosphate Dikinase

The pyruvate phosphate dikinase (PPDK) reaction mechanism is characterized by a distinct spatial separation of reaction centers and large conformational changes involving an opening-closing motion of the nucleotide-binding domain (NBD) and a swiveling motion of the central domain (CD). However, why PPDK is active only in a dimeric form and to what extent an alternate binding change mechanism could underlie this fact has remained elusive. We performed unbiased molecular dynamics simulations, configurational free energy computations, and rigidity analysis to address this question. Our results support the hypothesis that PPDK dimerization influences the opening-closing motion of the NBDs, and that this influence is mediated via the CDs of both chains. Such an influence would be a prerequisite for an alternate binding change mechanism to occur. To the best of our knowledge, this is the first time that a possible explanation has been suggested as to why only dimeric PPDK is active.

Essential role of the flexible linker on the conformational equilibrium of bacterial peroxiredoxin reductase for effective regeneration of peroxiredoxin

Reactive oxygen species (ROS) can damage DNA, proteins, and lipids, so cells have antioxidant systems that regulate ROS. In many bacteria, a dedicated peroxiredoxin reductase, alkyl hydroperoxide reductase subunit F (AhpF), catalyzes the rapid reduction of the redox-active disulfide center of the antioxidant protein peroxiredoxin (AhpC) to detoxify ROS such as hydrogen peroxide, organic hydroperoxide, and peroxynitrite. AhpF is a flexible multidomain protein that enables a series of electron transfers among the redox centers by accepting reducing equivalents from NADH. A flexible linker connecting the N-terminal domain (NTD) and C-terminal domain (CTD) of AhpF suggests that the enzyme adopts a large-scale domain motion that alternates between the closed and open states to shuttle electrons from the CTD via the NTD to AhpC. Here, we conducted comprehensive mutational, biochemical, and biophysical analyses to gain insights into the role of the flexible linker and the residues critical for the domain motions of Escherichia coli AhpF (EcAhpF) during electron transfer. Small-angle X-ray scattering studies of linker mutants revealed that a group of charged residues, 200EKR202, is crucial for the swiveling motion of the NTD. Moreover, NADH binding significantly affected EcAhpF flexibility and the movement of the NTD relative to the CTD. The mutants also exhibited a decrease in H2O2 reduction by the AhpF-AhpC ensemble. We propose that a concerted movement involving the NTD, C-terminal NADH, and FAD domains, and the flexible linker between them is essential for optimal intra-domain cross-talk and for efficient electron transfer to the redox partner AhpC required for peroxidation.

Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase

Pyruvate phosphate dikinase (PPDK) is a vital enzyme in cellular energy metabolism catalyzing the ATP- and P i -dependent formation of phosphoenolpyruvate from pyruvate in C4 -plants, but the reverse reaction forming ATP in bacteria and protozoa. The multi-domain enzyme is considered an efficient molecular machine that performs one of the largest single domain movements in proteins. However, a comprehensive understanding of the proposed swiveling domain motion has been limited by not knowing structural intermediates or molecular dynamics of the catalytic process. Here, we present crystal structures of PPDKs from Flaveria, a model genus for studying the evolution of C4 -enzymes from phylogenetic ancestors. These structures resolve yet unknown conformational intermediates and provide the first detailed view on the large conformational transitions of the protein in the catalytic cycle. Independently performed unrestrained MD simulations and configurational free energy calculations also identified these intermediates. In all, our experimental and computational data reveal strict coupling of the CD swiveling motion to the conformational state of the NBD. Moreover, structural asymmetries and nucleotide binding states in the PPDK dimer support an alternate binding change mechanism for this intriguing bioenergetic enzyme.

Rapid dynamics prediction of tool point for bi-rotary head five-axis machine tool

Receptance Coupling Substructure Analysis (RCSA), an effective approach to rapidly predict the tool point frequency response function (FRF), generally requires the response of spindle-machine assembly by experiments. This method is feasible for three-axis machine tool because the spindle and its posture are normally unchangeable. But in terms of five-axis milling, the spindle-machine assembly changes continuously. The purpose of this study is to propose new techniques to solve the constantly-changing assembly response in order that RCSA can be used for bi-rotary head five-axis machine tools. Based on receptance matrix determination in coupling direction and single degree of freedom coupling simplification, the swivel model for holder tip receptances is established for swivel motion. According to the concept of oriented frequency response function, the rotational model is derived to calculate the holder tip receptances with rotary motion. By combining the swivel model and the rotational model, the holder tip receptance of arbitrary posture can be calculated by three orthogonal postures. A five-axis machine tool with bi-rotary head is used to conduct FRF tests on different postures. Experimental results show that the models proposed can accurately predict tool point frequency response of any posture and large difference in FRFs among those postures of bi-rotary head is detected.

How vacuolar sorting receptor proteins interact with their cargo proteins: crystal structures of apo and cargo-bound forms of the protease-associated domain from an Arabidopsis vacuolar sorting receptor.

In plant cells, soluble proteins are directed to vacuoles because they contain vacuolar sorting determinants (VSDs) that are recognized by vacuolar sorting receptors (VSR). To understand how a VSR recognizes its cargo, we present the crystal structures of the protease-associated domain of VSR isoform 1 from Arabidopsis thaliana (VSR1PA) alone and complexed with a cognate peptide containing the barley (Hordeum vulgare) aleurain VSD sequence of 1ADSNPIRPVT10. The crystal structures show that VSR1PA binds the sequence, Ala-Asp-Ser, preceding the NPIR motif. A conserved cargo binding loop, with a consensus sequence of 95RGxCxF100, forms a cradle that accommodates the cargo-peptide. In particular, Arg-95 forms a hydrogen bond to the Ser-3 position of the VSD, and the essential role of Arg-95 and Ser-3 in receptor-cargo interaction was supported by a mutagenesis study. Cargo binding induces conformational changes that are propagated from the cargo binding loop to the C terminus via conserved residues in switch I-IV regions. The resulting 180° swivel motion of the C-terminal tail is stabilized by a hydrogen bond between Glu-24 and His-181. A mutagenesis study showed that these two residues are essential for cargo interaction and trafficking. Based on our structural and functional studies, we present a model of how VSRs recognize their cargos.

Thermodynamic dissection of large‐scale domain motions coupled with ligand binding of enzyme I

Domain motions are central to the biological functions of many proteins. The energetics of the motions, however, is often difficult to characterize when motions are coupled with the ligand binding. Here, we determined the thermodynamic parameters of individual domain motions and ligand binding of enzyme I (EI) using strategic domain-deletion mutants that selectively removed particular motions. Upon ligand binding, EI employs two large-scale domain motions, the hinge motion and the swivel motion, to switch between conformational states of distinct domain-domain orientations. Calorimetric analysis of the EI mutants separated the free energy changes of the binding and motions, demonstrating that the unfavorable hinge motion (ΔG = 1.5 kcal mol(-1)) was driven by the favorable swivel motion (ΔG = -5.2 kcal mol(-1)). The large free energy differences could be explained by the physicochemical nature of the domain interfaces associated with the motions; the hinge motion employed much narrower interface than the swivel motion without any hydrogen bonds or salt bridges. The small heat capacity further suggested that the packing of the domain interfaces associated with the hinge motion was less compact than that commonly observed in proteins. Lastly, thermodynamic analysis of phosphorylated EI suggests that the domain motions are regulated by the ligand binding and the phosphorylation states. Taken together, the thermodynamic dissection approach illustrates how multiple motions and ligand binding are energetically connected during the functional cycle of EI.

Structure of the guanylyltransferase domain of human mRNA capping enzyme

The enzyme guanylyltransferase (GTase) plays a central role in the three-step catalytic process of adding an (m7)GpppN cap cotranscriptionally to nascent mRNA (pre-mRNAs). The 5'-mRNA capping process is functionally and evolutionarily conserved from unicellular organisms to human. However, the GTases from viruses and yeast have low amino acid sequence identity (∼25%) with GTases from mammals that, in contrast, are highly conserved (∼98%). We have defined by limited proteolysis of human capping enzyme residues 229-567 as comprising the minimum enzymatically active human GTase (hGTase) domain and have determined the structure by X-ray crystallography. Seven related conformational states of hGTase exist in the crystal. The GTP-binding site is evolutionarily and structurally conserved. The positional variations of the oligonucleotide/oligosaccharide binding fold lid domain over the GTP-binding site provide snapshots of the opening and closing of the active site cleft through a swivel motion. The pattern of conserved surface residues in mammals, but not in yeast, supports the finding that the recognition of the capping apparatus by RNA polymerase II and associated transcription factors is highly conserved in mammals, and the mechanism may differ somewhat from that in yeast. The hGTase structure should help in the design of biochemical and molecular biology experiments to explore the proteinprotein and proteinRNA interactions that ensure regulated transcription of genes in humans and other mammals.

Molecular dynamics of zervamicin II and its analogs in water and methanol

A comparative study of the molecular dynamics of zervamicin II (an antimicrobial peptide from the peptaibol group, which has the channel-forming activity) in water and methanol has been performed. The influence of amino acid substitutions on the dynamics and stability of the peptide structure has been investigated. The amino acid sequence responsible for the absence of swivel motions in short peptaibols has been determined.

In-Vivo Remote Manipulation of Modified Capsule Endoscopes Using An External Magnetic Field

Background: Remote control of wireless capsule movement would enhance diagnostic accuracy and might allow targeted biopsy. The efficacy and safety of remote manipulation of modified capsule endoscopes using external magnetic fields were assessed in in-vivo survival studies in pigs as part of a European FP6 project called NEMO. Methods: Model and real wireless capsules (Colon & ESO, by Given Imaging Ltd) were modified to include magnetic material aligned to give different field patterns and strength when exposed to an external magnetic field. The magnetic reed switch in the capsule was inactivated to allow continuous real-time viewing. Capsules were placed in the esophagus and stomach of anesthetised pigs (n = 8, 34-78 kg). An external magnet was used to manipulate the capsule with gastroscopic visualisation. Capsules were attached to a thread to allow withdrawal through the cardio-esophageal junction and to measure forces needed to overcome magnetic attraction and peristaltic forces. The ability of a magnetic field to prevent retropulsion of an electrostimulation capsule causing esophageal contraction was tested. Anterior, lateral and posterior external magnet positions and movements were studied with the animals on the back, left lateral and prone positions. Results: An external plate magnet was effective in holding the capsule in specific locations in the esophagus. Swivel motions were particularly effective using small rotations of the external hand-held plate magnet allowing multiple axial panning circular views of the squamo-columnar junction to be obtained. Caudo-cranial axial magnet rotations caused capsules to somersault in the esophagus. Water lubrication enhanced esophageal capsule movement. In the stomach capsules could be manipulated at will throughout the stomach. It was possible but difficult to drive capsules through the cardio-esophageal junction and move capsules into the pylorus but not to release them in the duodenum by removing the magnetic field. Somersaulting and rapid exploration of the stomach was easy. The magnetic field prevented esophageal retropulsion of an electrostimulation capsule. All pigs were well, eating immediately after recovery - esophagus and stomach looked normal at follow up endoscopy. Left lateral position with a posterior hand held magnet was the best for most manipulations. Conclusions: Magnetic capsules could be swivelled, somersaulted, stopped and moved when constrained by an external magnetic field. Such movements were especially effective in enhancing visualization in the esophagus and stomach and were safe when the internal magnetic arrangement was matched to the external magnet and the size of the animal.

Swiveling Domain Mechanism in Pyruvate Phosphate Dikinase,

Pyruvate phosphate dikinase (PPDK) catalyzes the reversible conversion of phosphoenolpyruvate (PEP), AMP, and Pi to pyruvate and ATP. The enzyme contains two remotely located reaction centers: the nucleotide partial reaction takes place at the N-terminal domain, and the PEP/pyruvate partial reaction takes place at the C-terminal domain. A central domain, tethered to the N- and C-terminal domains by two closely associated linkers, contains a phosphorylatable histidine residue (His455). The molecular architecture suggests a swiveling domain mechanism that shuttles a phosphoryl group between the two reaction centers. In an early structure of PPDK from Clostridium symbiosum, the His445-containing domain (His domain) was positioned close to the nucleotide binding domain and did not contact the PEP/pyruvate-binding domain. Here, we present the crystal structure of a second conformational state of C. symbiosum PPDK with the His domain adjacent to the PEP-binding domain. The structure was obtained by producing a three-residue mutant protein (R219E/E271R/S262D) that introduces repulsion between the His and nucleotide-binding domains but preserves viable interactions with the PEP/pyruvate-binding domain. Accordingly, the mutant enzyme is competent in catalyzing the PEP/pyruvate half-reaction but the overall activity is abolished. The new structure confirms the swivel motion of the His domain. In addition, upon detachment from the His domain, the two nucleotide-binding subdomains undergo a hinge motion that opens the active-site cleft. A similar hinge motion is expected to accompany nucleotide binding (cleft closure) and release (cleft opening). A model of the coupled swivel and cleft opening motions was generated by interpolation between two end conformations, each with His455 positioned for phosphoryl group transfer from/to one of the substrates. The trajectory of the His domain avoids major clashes with the partner domains while preserving the association of the two linker segments.

Surface-modulated motion switch: Capture and release of iron–sulfur protein in the cytochrome bc 1 complex

In the cytochrome bc(1) complex, the swivel motion of the iron-sulfur protein (ISP) between two redox sites constitutes a key component of the mechanism that achieves the separation of the two electrons in a substrate molecule at the quinol oxidation (Q(o)) site. The question remaining is how the motion of ISP is controlled so that only one electron enters the thermodynamically favorable chain via ISP. An analysis of eight structures of mitochondrial bc(1) with bound Q(o) site inhibitors revealed that the presence of inhibitors causes a bidirectional repositioning of the cd1 helix in the cytochrome b subunit. As the cd1 helix forms a major part of the ISP binding crater, any positional shift of this helix modulates the ability of cytochrome b to bind ISP. The analysis also suggests a mechanism for reversal of the ISP fixation when the shape complementarity is significantly reduced after a positional reorientation of the reaction product quinone. The importance of shape complementarity in this mechanism was confirmed by functional studies of bc(1) mutants and by a structure determination of the bacterial form of bc(1). A mechanism for the high fidelity of the bifurcated electron transfer is proposed.